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- PDB-4uj5: Crystal structure of human Rab11-Rabin8-FIP3 -

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Basic information

Entry
Database: PDB / ID: 4uj5
TitleCrystal structure of human Rab11-Rabin8-FIP3
Components
  • RAB-3A-INTERACTING PROTEIN
  • RAS-RELATED PROTEIN RAB-11A
KeywordsTRANSPORT PROTEIN / CILIARY TARGETING COMPLEX / CILIUM / VESICU TRANSPORT / MEMBRANE TRAFFICKING / RABIN8 / RAB11 / FIP3
Function / homology
Function and homology information


Golgi to plasma membrane transport vesicle / ciliary basal body-plasma membrane docking / regulation of early endosome to recycling endosome transport / regulation of protein localization to centrosome / regulation of multivesicular body size / regulation of endocytic recycling / postsynaptic recycling endosome / establishment of protein localization to organelle / protein localization to organelle / plasma membrane to endosome transport ...Golgi to plasma membrane transport vesicle / ciliary basal body-plasma membrane docking / regulation of early endosome to recycling endosome transport / regulation of protein localization to centrosome / regulation of multivesicular body size / regulation of endocytic recycling / postsynaptic recycling endosome / establishment of protein localization to organelle / protein localization to organelle / plasma membrane to endosome transport / establishment of vesicle localization / negative regulation of filopodium assembly / regulation of cilium assembly / exosomal secretion / amyloid-beta clearance by transcytosis / melanosome transport / astral microtubule organization / proximal dendrite / VxPx cargo-targeting to cilium / neurotransmitter receptor transport, endosome to postsynaptic membrane / BBSome-mediated cargo-targeting to cilium / regulation of vesicle-mediated transport / Golgi to plasma membrane transport / RAB geranylgeranylation / myosin V binding / protein localization to cilium / RAB GEFs exchange GTP for GDP on RABs / multivesicular body assembly / dynein light intermediate chain binding / establishment of protein localization to membrane / protein localization to cell surface / TBC/RABGAPs / protein targeting to membrane / syntaxin binding / mitotic metaphase chromosome alignment / positive regulation of epithelial cell migration / exocytosis / cleavage furrow / cilium assembly / centriolar satellite / mitotic spindle assembly / phagocytic vesicle / transport vesicle / vesicle-mediated transport / Anchoring of the basal body to the plasma membrane / positive regulation of G2/M transition of mitotic cell cycle / centriole / multivesicular body / guanyl-nucleotide exchange factor activity / small monomeric GTPase / G protein activity / trans-Golgi network membrane / ciliary basal body / regulation of cytokinesis / Translocation of SLC2A4 (GLUT4) to the plasma membrane / protein localization to plasma membrane / trans-Golgi network / cytoplasmic vesicle membrane / recycling endosome / Vasopressin regulates renal water homeostasis via Aquaporins / spindle pole / recycling endosome membrane / neuron projection development / endocytic vesicle membrane / protein transport / GTPase binding / lamellipodium / cytoplasmic vesicle / microtubule binding / vesicle / Golgi membrane / intracellular membrane-bounded organelle / GTPase activity / centrosome / glutamatergic synapse / GTP binding / perinuclear region of cytoplasm / Golgi apparatus / protein-containing complex / extracellular exosome / identical protein binding / nucleus / cytosol
Similarity search - Function
GDP/GTP exchange factor Sec2, N-terminal / Guanine nucleotide exchange factor RAB3IL/RAB3IP/Sec2 / GDP/GTP exchange factor Sec2p / small GTPase Rab1 family profile. / Ran (Ras-related nuclear proteins) /TC4 subfamily of small GTPases / Rho (Ras homology) subfamily of Ras-like small GTPases / Ras subfamily of RAS small GTPases / Small GTPase / Ras family / Rab subfamily of small GTPases ...GDP/GTP exchange factor Sec2, N-terminal / Guanine nucleotide exchange factor RAB3IL/RAB3IP/Sec2 / GDP/GTP exchange factor Sec2p / small GTPase Rab1 family profile. / Ran (Ras-related nuclear proteins) /TC4 subfamily of small GTPases / Rho (Ras homology) subfamily of Ras-like small GTPases / Ras subfamily of RAS small GTPases / Small GTPase / Ras family / Rab subfamily of small GTPases / Small GTP-binding protein domain / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / Ras-related protein Rab-11A / Rab-3A-interacting protein
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.604 Å
AuthorsVetter, M. / Lorentzen, E.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2015
Title: Structure of Rab11-Fip3-Rabin8 Reveals Simultaneous Binding of Fip3 and Rabin8 Effectors to Rab11.
Authors: Vetter, M. / Stehle, R. / Basquin, C. / Lorentzen, E.
History
DepositionApr 8, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 12, 2015Provider: repository / Type: Initial release
Revision 1.1Aug 19, 2015Group: Database references
Revision 1.2Sep 16, 2015Group: Database references
Revision 1.3Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RAS-RELATED PROTEIN RAB-11A
B: RAS-RELATED PROTEIN RAB-11A
C: RAB-3A-INTERACTING PROTEIN
D: RAB-3A-INTERACTING PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,3139
Polymers86,1244
Non-polymers1,1895
Water2,864159
1
A: RAS-RELATED PROTEIN RAB-11A
C: RAB-3A-INTERACTING PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,7045
Polymers43,0622
Non-polymers6433
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1500 Å2
ΔGint-8.4 kcal/mol
Surface area21010 Å2
MethodPQS
2
B: RAS-RELATED PROTEIN RAB-11A
D: RAB-3A-INTERACTING PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,6084
Polymers43,0622
Non-polymers5472
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1340 Å2
ΔGint-8.3 kcal/mol
Surface area20290 Å2
MethodPQS
Unit cell
Length a, b, c (Å)51.683, 108.202, 75.736
Angle α, β, γ (deg.)90.00, 102.83, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
22
/ NCS ensembles :
ID
1
2

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Components

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Protein , 2 types, 4 molecules ABCD

#1: Protein RAS-RELATED PROTEIN RAB-11A / RAB-11 / YL8 / RAB-11 / YL8 / RAB11A


Mass: 20844.451 Da / Num. of mol.: 2 / Fragment: GTPASE DOMAIN, RESIDUES 6-186 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PET / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P62491
#2: Protein RAB-3A-INTERACTING PROTEIN / RAB3A-INTERACTING PROTEIN / RABIN-3 / SSX2-INTERACTING PROTEIN / RAB3A-INTERACTING PROTEIN / RABIN- ...RAB3A-INTERACTING PROTEIN / RABIN-3 / SSX2-INTERACTING PROTEIN / RAB3A-INTERACTING PROTEIN / RABIN-3 / SSX2-INTERACTING PROTEIN / RABIN8


Mass: 22217.479 Da / Num. of mol.: 2 / Fragment: C-TERMINAL DOMAIN, RESIDUES 286-476
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PET / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q96QF0

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Non-polymers , 4 types, 164 molecules

#3: Chemical ChemComp-GNP / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / 5'-Guanylyl imidodiphosphate


Mass: 522.196 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N6O13P3
Comment: GppNHp, GMPPNP, energy-carrying molecule analogue*YM
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 159 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsQ70L POINT MUTATION

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.52 Å3/Da / Density % sol: 51 % / Description: NONE
Crystal growpH: 7
Details: 0.1M HEPES PH 7.0, 0.2M LITHIUM SULFATE AND 24% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1
DetectorType: DECTRIS PILATUS / Detector: PIXEL
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.53→50 Å / Num. obs: 24951 / % possible obs: 94 % / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Biso Wilson estimate: 69.6 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 14
Reflection shellResolution: 2.53→2.69 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.74 / Mean I/σ(I) obs: 1 / % possible all: 84

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1YZK

1yzk


Resolution: 2.604→43.642 Å / SU ML: 0.49 / σ(F): 1.93 / Phase error: 34.25 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2716 2270 5 %
Rwork0.2146 --
obs0.2174 24374 92.19 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.604→43.642 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5111 0 71 159 5341
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0055302
X-RAY DIFFRACTIONf_angle_d1.0727223
X-RAY DIFFRACTIONf_dihedral_angle_d14.0651857
X-RAY DIFFRACTIONf_chiral_restr0.039830
X-RAY DIFFRACTIONf_plane_restr0.004915
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6035-2.66010.41261370.38872551X-RAY DIFFRACTION88
2.6601-2.7220.39951460.36932718X-RAY DIFFRACTION92
2.722-2.79010.43291400.36682591X-RAY DIFFRACTION91
2.7901-2.86550.36011370.34992628X-RAY DIFFRACTION89
2.8655-2.94980.42331350.33282579X-RAY DIFFRACTION90
2.9498-3.0450.37071460.29732749X-RAY DIFFRACTION93
3.045-3.15380.30691480.25962798X-RAY DIFFRACTION96
3.1538-3.280.27741480.23552766X-RAY DIFFRACTION95
3.28-3.42920.30411470.2382761X-RAY DIFFRACTION95
3.4292-3.60990.27821440.21512734X-RAY DIFFRACTION94
3.6099-3.8360.25661430.20062689X-RAY DIFFRACTION93
3.836-4.1320.27231440.20082646X-RAY DIFFRACTION90
4.132-4.54740.26171290.17432651X-RAY DIFFRACTION91
4.5474-5.20450.24351390.18032672X-RAY DIFFRACTION92
5.2045-6.55350.25871490.20852729X-RAY DIFFRACTION94
6.5535-43.64810.19681380.16662639X-RAY DIFFRACTION91

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